mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-08-30 16:58:03 +08:00
James Taylor
121 lines
4.4 KiB
Python
121 lines
4.4 KiB
Python
from galaxy.test.base.twilltestcase import TwillTestCase
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# the numbering of the tests is essential as they
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# will be executed in order, sorted by name
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class Operations(TwillTestCase):
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def test_00_first(self): # must be first
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"Uploading data"
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self.clear_history()
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self.upload_file('1.bed', dbkey='hg17')
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self.upload_file('2.bed', dbkey='hg17')
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def test_intersect(self):
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"Intersect"
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self.run_tool('Intersect1', input1='1.bed', input2="2.bed", min=1)
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self.check_data('op-intersect.dat')
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def test_join(self):
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"Join"
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self.run_tool('Join1', input1='1.bed', input2="2.bed", min=1)
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self.check_data('op-join.dat')
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def test_merge(self):
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"Merge"
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self.run_tool('Merge1', input='1.bed')
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self.check_data('op-merge.dat')
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def test_overlap(self):
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"Overlap"
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self.run_tool('Overlap1', input1='1.bed', input2="2.bed", min=1)
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self.check_data('op-overlap.dat')
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def test_proximity(self):
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"Proximity"
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self.run_tool('Proximity1', input1='1.bed', input2="2.bed", within="-within", up=0, down=0)
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self.check_data('op-proximity.dat')
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def test_subtract(self):
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"Subtract"
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self.run_tool('Subtract1', input1='1.bed', input2="2.bed")
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self.check_data('op-subtract.dat')
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def test_union(self):
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"Union"
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self.run_tool('Union2', input1='1.bed', input2="2.bed")
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self.check_data('op-union.dat')
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def test_cluster(self):
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"Cluster"
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self.run_tool('Cluster1', input='1.bed', num=2, size=10)
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self.check_data('op-cluster.dat')
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def test_clustermerge(self):
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"Cluster merge"
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self.run_tool('ClusterMerge1', input='1.bed', num=2, size=10)
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self.check_data( 'op-clustermerge.dat')
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def test_complement(self):
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"Complement"
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self.run_tool('Complement1', input='1.bed')
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self.check_data('op-complement.dat')
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def test_interval_complement(self):
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"Interval Complement"
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self.run_tool('interval_complement1', input='1.bed')
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self.check_data('op-interval-complement.dat')
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def test_covdens(self):
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"covDensity"
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self.run_tool('covDensity1', input1='1.bed', input2="2.bed")
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self.check_data('op-covdensity.dat')
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def test_interval_covdens(self):
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"Interval covDensity"
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self.run_tool('interval_coverage', input1='1.bed')
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self.check_data('op-interval-covdensity.dat')
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def test_difference(self):
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"Difference"
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self.run_tool('Difference1', input1='1.bed', input2="2.bed")
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self.check_data('op-difference.dat')
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def test_extend(self):
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"Extend"
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self.run_tool('Extend1', input='1.bed', len=100, where="ud")
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self.check_data('op-extend.dat')
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def test_zz_fill_the_queue(self): # must be last (when sorted on the name)
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"Stress test, running all operations"
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self.test_00_first()
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self.run_tool('Intersect1', input1='1.bed', input2="2.bed", min=1)
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self.run_tool('Join1', input1='1.bed', input2="2.bed", min=1)
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self.run_tool('Merge1', input='1.bed')
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self.run_tool('Overlap1', input1='1.bed', input2="2.bed", min=1)
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self.run_tool('Proximity1', input1='1.bed', input2="2.bed", within="-within", up=0, down=0)
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self.run_tool('Subtract1', input1='1.bed', input2="2.bed")
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self.run_tool('Union2', input1='1.bed', input2="2.bed")
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self.run_tool('Cluster1', input='1.bed', num=2, size=10)
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self.run_tool('ClusterMerge1', input='1.bed', num=2, size=10)
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self.run_tool('Complement1', input='1.bed')
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self.run_tool('covDensity1', input1='1.bed', input2="2.bed")
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self.run_tool('Difference1', input1='1.bed', input2="2.bed")
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self.run_tool('interval_complement1', input='1.bed')
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self.run_tool('interval_coverage', input1='1.bed')
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self.run_tool('Extend1', input='1.bed', len=100, where="ud")
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self.wait()
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names = [
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'op-intersect.dat','op-join.dat', 'op-merge.dat', 'op-overlap.dat',
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'op-proximity.dat', 'op-subtract.dat', 'op-union.dat', 'op-cluster.dat',
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'op-clustermerge.dat', 'op-complement.dat', 'op-covdensity.dat', 'op-difference.dat',
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'op-interval-complement.dat', 'op-interval-covdensity.dat', 'op-extend.dat'
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]
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for idx, name in enumerate(names):
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self.check_data(name, hid=idx+3, wait=False)
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